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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacgcttttgcttactgttacaatttacaaagctgtctgacttacacaaaatactgtcattctatactag

Basic information

species Oryza sativa
transcript LOC_Os04g59494.2
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G376731_T01 (Zea mays), 5'ss of exon 26
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacg-------cttttgcttactgttacaat-ttacaaagctgtctga-cttacac-aaaatactgtcattctatactag
|||  |||||||||||||||||||||| || || ||||| || |||||||||||| ||  |         ||  || |||  | | || | || |  | |||  ||| |||   |  ||||  | |     || || ||
GATCAGAGATGATTTTGAGAAAGAGGACGCGTTTCATGGACTGTGTGCAATGgtatatgtatatccagacctcctggttatggctgcattcttccttatctgggtgatcttgttctgaaatcttatttggttacaccag

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA20G24040.1 (Glycine max), 5'ss of exon 26
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacgcttttgcttactgttacaatttacaaagctgtctgacttacacaaaatactgtcattctatactag-------
||||||||||||| |||||||||||||||| ||    ||||||||||| ||||||       |||  |  | |||  |  |||||      |     |||||  | |  |   ||| ||| || | | |       
GATACGAGATGATGTTGAGAAAGAGGATGCTTTTAGAGGTCTATGTGCTATGgtat------gctcctattcact-ctgtaattttttttacatgtagacttgtaaagtaatttgt-attttacatttgttttcag

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA10G42960.1 (Glycine max), 5'ss of exon 26
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacgcttttgcttactgttacaatttacaaagctgtctgacttacacaaaatactgtcattctatactag-------
||||||||||||| |||||||||||||||| ||    ||||||||||| ||||||       |||  |  | ||||    |||||   |   |||  |||||  | |  |    |  ||| || | | |       
GATACGAGATGATGTTGAGAAAGAGGATGCTTTTAGAGGTCTATGTGCTATGgtat------gctcctattcactgggtaaattttttaca-tgta-gacttgtaaagtaattgggtattttacatttgttttcag

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 26
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 5'ss of exon 26
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacgcttt------tgcttactgttacaatttacaaagctgtctgacttacacaaaatactgtcattctatactag
|||||| |||||| ||||||| || ||||| |||| ||||||||||||||  |||     |  ||||      | |||| |     |  | | | |  | | |   ||  |   |||   |   |   ||   ||
GATACGTGATGATATTGAGAAGGAAGATGCCTTCCGTGGTCTATGTGCAACTgtatgcaaattctttcttgattccttagtagatgagatcaaagaaatatatatattgtaattaatgaagcattggaattgcag

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 26
lower sequence: PP1S276_77V6.1 (Physcomitrella patens), 5'ss of exon 26
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatc---cacgcttttgcttactg---------ttacaatttacaaagctgtctgacttac--acaaaatactgtcattctatactag---------------------------------------------------
|||||||||||||||||||||||| ||||| || |  || || ||||| |||||| ||    ||        |  ||              || | |  |||||  | |     |   |||| || || ||||   ||   ||                                                   
GATACGAGATGATTTTGAGAAAGAAGATGCTTTTCGAGGCCTGTGTGCTATGgtatatttcgcagatcacaaccaaccaggaacatatccgcattatcgaaagccattttttagattgacaagatgctttcatagaattgaaggaaatttattaaaaagtgtcgactaattgatcgtgtggggtggtatattag

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 5'ss of exon 26
lower sequence: PP1S41_175V6.1 (Physcomitrella patens), 5'ss of exon 25
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacgcttt-tgcttac--------tgttacaatttacaaagctgtctgacttacacaaaatactgtcattc--tatactag------------
||||||||||||||||||||| || ||||||||||  ||  | ||||| ||||||      |  ||| || ||||        | |  ||| || ||    |  |||  | |     | | | ||  | |  | |  |||            
GATACGAGATGATTTTGAGAAGGAAGATGCATTCCGGGGCTTGTGTGCCATGgtatgatggctttttgtggttacataagttttatggcaacttgcagctgttcctgtttgaattggagttcagtgctcccttgttttagaattcttctgat

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATACGAGATGATTTTGAGAAAGAGGATGCATTCCATGGTCTATGTGCAATGgtacatccacgcttttgcttactgttacaatttacaaagctgtctgacttacacaaaatactgtcattctatactag

- -  GAGATG
- - - - - - - - - - AAGAGG
- - - - - - - - - -  AGAGGA
- - - - - - - - - - - GAGGAT
- - - - - - - - - - -  AGGATG